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THE MOLECULAR CHARACTERIZATION of the VIRUS and VIRUS-LIKE AGENTS PRESENT in TA TAO 5 GERMPLASM of PRUNUS PERSICA Diana Marini Clemson University, [email protected]

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THE MOLECULAR CHARACTERIZATION of the VIRUS and VIRUS-LIKE AGENTS PRESENT in TA TAO 5 GERMPLASM of PRUNUS PERSICA Diana Marini Clemson University, Dmarini@Clemson.Edu Clemson University TigerPrints All Dissertations Dissertations 12-2007 THE MOLECULAR CHARACTERIZATION OF THE VIRUS AND VIRUS-LIKE AGENTS PRESENT IN TA TAO 5 GERMPLASM OF PRUNUS PERSICA Diana Marini Clemson University, [email protected] Follow this and additional works at: https://tigerprints.clemson.edu/all_dissertations Part of the Agronomy and Crop Sciences Commons Recommended Citation Marini, Diana, "THE MOLECULAR CHARACTERIZATION OF THE VIRUS AND VIRUS-LIKE AGENTS PRESENT IN TA TAO 5 GERMPLASM OF PRUNUS PERSICA " (2007). All Dissertations. 143. https://tigerprints.clemson.edu/all_dissertations/143 This Dissertation is brought to you for free and open access by the Dissertations at TigerPrints. It has been accepted for inclusion in All Dissertations by an authorized administrator of TigerPrints. For more information, please contact [email protected]. THE MOLECULAR CHARACTERIZATION OF THE VIRUS AND VIRUS-LIKE AGENTS PRESENT IN TA TAO 5 GERMPLASM OF PRUNUS PERSICA A Dissertation Presented to the Graduate School of Clemson University In Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy Plant and Environmental Sciences by Diana Beatriz Marini December 2007 Accepted by: Dr. Simon W. Scott, Committee Chair Dr. N. Dwight Camper Dr. Steven N. Jeffers Dr. Gregory L. Reighard ABSTRACT Peach production in the southeastern United States is limited by late spring freezes. Ta Tao 5 germplasm, used either as an interstem or by chip bud inoculation, has been shown to delay bloom and avoid the effects of these late freezes. The growth modification is graft transmissible and the germplasm has been found to be infected with ACLSV, APruV-3, and PLMVd. Using a combination of PCR, cloning, and sequencing techniques, a molecular characterization of the three graft-transmissible agents present in Ta Tao 5 has been completed. The complete nucleotide sequence of the genome of the isolate of ACLSV (ACLSV-Ta Tao 5) was determined. The genomic organization was typical of other isolates of ACLSV, but the sequence showed only 73% nucleotide identity to the Batalon1 isolate of ACLSV. This distant relationship with characterized isolates of ACLSV explains why primers recommended for PCR reactions used to identify the virus failed to detect the isolate from Ta Tao 5 reliably. This is the first complete genomic sequence of an isolate of ACLSV from peach. The 3’ terminal third of the complete sequence of APruV-3 isolated from Ta Tao 5 was obtained. Four ORFs and one long 819 nt NCR region were identified. The ORFs encoded for the TGB proteins and the CP, respectively. The aa sequence of the CP showed 94% identity with the corresponding published sequence of APruV- 3. ii The genome of the isolate of PLMVd present in Ta Tao 5 was 337 nt in length and showed no obvious insertions or variations. The sequence showed more than 96% sequence identity with PLMVd isolates found in other parts of the world. Reliable and sensitive techniques for the detection of the agents infecting Ta Tao 5 are described in this study. One-Step PCR was used to detect all three agents, and PLMVd also was detected readily by dot blot hybridization. The further studies necessary to determine the relationship between these three agents found in Ta Tao 5 and the bloom delay phenomenon now can be completed. iii DEDICATION This dissertation is dedicated to my husband, Antonio, who always encourages me to be a better person; to my children, Luz, Joaquin, and Nicolas, who are inexhaustible sources of happiness and help me forget any frustration; to my parents, Anita and Juan, who taught me the value of the simple things of life; to my mother-in-law, Pirucha, for her friendship and for helping with the children while I was studying; and to my sisters, Silvia and Ana, for their love and support. iv ACKNOWLEDGEMENTS I wish to especially thank to my advisor, Dr. Simon Scott, who with a lot of patience, encouraged, supported and guided me throughout these years and who is not only an excellent virologist but also a great person. I also thank the other members of my advisory committee for helpful advice and suggestions: Dr. Dwight Camper, Dr. Steven Jeffers, and Dr. Greg Reighard. A special thanks to Dr. Phil Gibson, not only for his great help with many laboratory and field activities, but also for his friendship and camaraderie. I also would like to thank M. Tracy Zimmerman, who, with a lot of patience, taught and assisted me with molecular techniques and procedures. The technical assistance of Jane Lawrence, Kathy Brock, and Dave Ouellette are gratefully acknowledged. I wish to thank the Instituto Nacional de Tecnologia Agropecuaria (INTA) from Argentina, for sending me and partially financing my stay in US. Finally, I would like to thank for their help and friendship the many professors, students, and staff in the Department of Entomology, Soils, and Plant Sciences at Clemson University. v TABLE OF CONTENTS Page TITLE PAGE ....................................................................................................... i ABSTRACT ........................................................................................................ ii DEDICATION .................................................................................................... iv ACKNOWLEDGEMENTS .................................................................................. v LIST OF TABLES ............................................................................................ viii LIST OF FIGURES ........................................................................................... x CHAPTERS I. INTRODUCTION ............................................................................... 1 II. LITERATURE REVIEW ..................................................................... 4 Stone Fruit Characteristics and Economic Importance ...................... 5 The Peach ......................................................................................... 6 Peach Production in the Southeastern United States ........................ 8 Use of Peach Interstems to Alter Peach Phenology ........................ 10 Graft-Transmissible Agents in Ta Tao Germplasm and Bloom Delay ............................................................................... 12 Filamentous Viruses that Infect Stone Fruits ................................... 18 Viroids that Infect Stone Fruits ......................................................... 29 Virus and Viroid Detection Methods ................................................. 38 III. MOLECULAR CHARACTERIZATION OF THE ISOLATE OF APPLE CHLOROTIC LEAF SPOT VIRUS (ACLSV) PRESENT IN TA TAO 5 GERMPLASM OF PRUNUS PERSICA .............................................................. 62 Introduction ...................................................................................... 62 Materials and Methods ..................................................................... 63 Results ............................................................................................. 69 Discussion ....................................................................................... 74 vi Table of Contents (Continued) Page IV. MOLECULAR CHARACTERIZATION OF THE ASIAN PRUNUS VIRUS (APruV) ISOLATE PRESENT IN TA TAO 5 ................................................................................... 94 Introduction ...................................................................................... 94 Materials and Methods ..................................................................... 97 Results ........................................................................................... 100 Discussion ..................................................................................... 102 V. MOLECULAR CHARACTERIZATION OF THE PEACH LATENT MOSAIC VIROID (PLMVd) ISOLATE PRESENT IN TA TAO 5 ........................................................... 119 Introduction .................................................................................... 119 Materials and Methods ................................................................... 122 Results ........................................................................................... 124 Discussion ..................................................................................... 125 VI. CONCLUSIONS ............................................................................ 135 APPENDICES ................................................................................................ 139 REFERENCES .............................................................................................. 163 vii LIST OF TABLES Table Page 2.1 Ta Tao genotypes of peach (Prunus persica) imported into the US through the USDA Plant Introduction Station, Chico, California in 1933 ............................................... 59 2.2 Cultivars of Prunus spp. from which the six original isolates of virus that cross-reacted with antibodies to plum pox virus originated ........................................................ 60 2.3 Genera and viruses included within the family Flexiviridae .............. 61 3.1 Viral sequences used for comparison in this study .......................... 78 3.2 Sequences of the primers used to detect and clone the isolate of apple chlorotic leaf spot virus (ACLSV) from Ta Tao 5 peach (Prunus persica) germplasm ............................ 79 3.3 A comparison of the percentage identity of the putative amino acid (aa) sequences of the RNA dependent RNA polymerase (RdRp),
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